diff --git a/src/bcftools/bcftools_concat/script.sh b/src/bcftools/bcftools_concat/script.sh index e69de29b..6cd9d4db 100644 --- a/src/bcftools/bcftools_concat/script.sh +++ b/src/bcftools/bcftools_concat/script.sh @@ -0,0 +1,46 @@ +#!/bin/bash + +## VIASH START +## VIASH END + +# Exit on error +set -eo pipefail + +# Unset parameters +unset_if_false=( + par_allow_overlaps + par_compact_PS + par_ligate + par_ligate_force + par_ligate_warn + par_no_version + par_naive + par_naive_force +) + +for par in ${unset_if_false[@]}; do + test_val="${!par}" + [[ "$test_val" == "false" ]] && unset $par +done + +# Execute bcftools concat with the provided arguments +bcftools concat \ + ${par_allow_overlaps:+-a} \ + ${par_compact_PS:+-c} \ + ${par_remove_duplicates:+-d "$par_remove_duplicates"} \ + ${par_file_list:+-f "$par_file_list"} \ + ${par_ligate:+-l} \ + ${par_ligate_force:+--ligate-force} \ + ${par_ligate_warn:+--ligate-warn} \ + ${par_no_version:+--no-version} \ + ${par_naive:+-n} \ + ${par_naive_force:+--naive-force} \ + ${par_output_type:+--O "$par_output_type"} \ + ${par_min_PQ:+-q "$par_min_PQ"} \ + ${par_regions:+-r "$par_regions"} \ + ${par_regions_file:+-R "$par_regions_file"} \ + ${par_regions_overlap:+--regions-overlap "$par_regions_overlap"} \ + ${par_threads:+--threads "$par_threads"} \ + ${par_verbose:+-v "$par_verbose"} \ + -o $par_output \ + $par_input \ No newline at end of file